Good points.
Short answer is, not 2D, this takes into account 3D, which ever view you have of a car, top or side, it should match the aero template. The current models of the VW Scirocco and Volvo C30 bring home how this works in top view the best.
Bottom line is this is the shape that offers the lowest Cd potential if a vehicle were to be shaped like it. Obviously, they're not. This template is intended to be a guide for someone who wants to add something to the back end of their vehicle to improve the Cd. You overlay the outline and cut to the dotted line, what ever you build to fill in the blank, should then be an optimized improvement to the previous shape you had.
Here is a recent 88 B2000 Mazda P/U I did this overlay on.
So if a guy were to build a cap on his cargo bed shaped to match this line, it would be the best compromise between too steep and too shallow of an angle along the top.
Yer welcome to try and explain why a different shape would be better, this one is the product of a very keen persons lifetime of work and thought in the realm of aerodynamics. He may be wrong. But I'd bet real money and body parts that he's really close, and in this game, really close will get you the result you're after when it comes to trying to improve the aerodynamics of a bluff body in ground effect, deviate from it at your own peril.
Look around you at most of the current European cars as you're out and about, you'll see their roof lines in profile match this template almost universally, funny that.